Contacts of the strand formed by residues 180 - 186 (chain A) in PDB entry 1QCY
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with GLN 180 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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143A LEU 2.9 7.4 + - - +
144A ASP* 3.1 13.7 - - - +
145A ILE* 2.8 27.8 + - - +
174A ILE* 4.4 2.9 - - - -
175A GLY 3.7 15.5 - - - +
176A PRO* 4.0 19.4 - - - +
179A THR* 1.3 73.7 - - - +
181A VAL* 1.3 66.0 + - - +
196A LEU* 3.2 26.6 + - + +
197A ASN* 3.5 20.4 - - - +
199A TYR 5.3 4.6 + - - +
239A GLY 2.9 16.1 + - - +
241A ARG* 2.8 38.9 - - - +
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Residues in contact with VAL 181 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145A ILE* 3.2 13.5 - - + +
147A ILE* 4.4 6.5 - - + -
169A LEU* 4.1 26.9 - - + -
172A MET* 4.3 9.4 - - - -
174A ILE* 3.7 29.2 - - + +
179A THR* 4.4 2.2 - - + -
180A GLN* 1.3 81.4 - - - +
182A GLY* 1.3 71.6 + - - +
183A ILE* 4.2 13.5 - - + -
194A PHE* 3.4 19.3 - - + -
195A ASN 3.5 10.4 - - - +
196A LEU* 3.5 9.7 + - - +
199A TYR* 5.6 2.6 + - - +
205A VAL* 4.6 14.2 - - + +
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Residues in contact with GLY 182 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145A ILE 2.8 9.4 + - - +
146A VAL* 3.2 10.0 - - - -
147A ILE 2.9 23.6 + - - -
181A VAL* 1.3 75.3 - - - +
183A ILE* 1.3 65.5 + - - +
184A VAL* 5.6 0.4 - - - -
194A PHE* 3.4 14.4 - - - -
196A LEU* 3.5 16.5 - - - +
233A ALA* 6.4 0.7 - - - -
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Residues in contact with ILE 183 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147A ILE* 3.4 29.6 - - + +
149A LEU* 4.3 14.8 - - + -
165A LEU* 4.3 14.1 - - + -
169A LEU* 4.6 9.0 - - + -
181A VAL* 4.2 5.2 - - + -
182A GLY* 1.3 80.6 - - - +
184A VAL* 1.3 72.7 + - - +
192A HIS* 3.8 1.2 - - - -
193A GLU* 2.9 32.8 + - + -
194A PHE* 3.1 47.9 + - + +
209A ALA* 4.7 1.8 - - + -
212A ILE* 3.8 26.2 - - + -
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Residues in contact with VAL 184 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146A VAL* 4.3 6.5 - - + -
147A ILE 2.8 11.4 + - - +
148A VAL* 3.3 11.6 - - + +
149A LEU* 2.8 27.0 + - - +
182A GLY 5.6 0.2 - - - -
183A ILE* 1.3 80.9 - - - +
185A GLN* 1.3 64.9 + - - +
186A TYR* 5.2 0.7 - - + -
190A VAL* 3.4 31.9 - - + -
191A THR 3.5 5.4 - - - +
192A HIS* 3.8 31.6 - - + +
225A GLY 4.5 11.7 - - - +
228A THR* 5.4 0.2 - - + -
229A ALA* 4.7 5.4 - - + +
233A ALA* 4.2 15.0 - - + -
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Residues in contact with GLN 185 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149A LEU* 3.3 18.2 - - + +
151A GLY* 3.3 21.4 - - - -
158A TRP* 3.9 7.2 - - - -
184A VAL* 1.3 75.5 - - - +
186A TYR* 1.3 66.5 + - - +
189A ASN 4.0 0.3 - - - +
190A VAL* 3.6 1.2 - - - +
191A THR* 2.9 34.8 + - - +
193A GLU* 2.6 39.0 + - + +
212A ILE* 3.8 8.6 - - + +
213A VAL 2.9 21.3 + - - +
214A GLN* 3.5 3.3 - - - -
215A ARG* 2.8 42.3 + - + +
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Residues in contact with TYR 186 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148A VAL* 3.5 33.2 - - + -
149A LEU 2.8 11.9 + - - -
150A ASP* 3.5 22.3 - - - +
151A GLY* 2.7 31.8 + - - -
184A VAL* 5.2 0.2 - - + -
185A GLN* 1.3 78.0 - - - +
187A GLY* 1.3 62.4 + - - +
189A ASN 3.1 11.2 - - - +
190A VAL* 3.9 17.9 - - + -
215A ARG* 6.4 0.9 - - - -
220A THR* 3.5 23.3 - - + -
221A MET* 3.4 15.3 - - + +
222A THR* 2.9 36.7 + - + +
225A GLY* 3.9 8.7 - - - +
250A ILE* 4.6 4.9 - - + +
251A VAL 4.2 1.2 + - - -
252A THR* 3.4 23.0 + - - -
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il